Difference between revisions of "DNA Melting Report Requirements for Part 1"

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[[Category:20.309]]
 
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[[Category:DNA Melting Lab]]
 
[[Category:DNA Melting Lab]]
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==Report requirements==
 
==Report requirements==
#Plot fluorescence versus time for one minute and estimate the noise level by calculating the variance.  
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* One member of your group should submit a single PDF file to Stellar in advance of the deadline. The filename should consist of the last names of all group members, CamelCased, in alphabetical order, with a .pdf extension. Example: <code>CrickFranklinWatson.pdf</code>.
#Using the same amplifier gain, estimate the change in signal between DNA sample in and sample out.
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* Include answers to questions embedded in the lab manual (e.g. the questions in the RTD section)
##What is the signal to noise ratio (SNR) in units of dB for your system?
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* The file must be less than 20 MB.
##Ensure that your system has an SNR of at least 12 dB.
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* Include code at the end of the document in an appendix, in the same pdf file, not as as separate upload.
#Obtain a DNA melting curve by plotting fluorescence versus temperature.  
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* Not counting the appendix, your report should be no longer than 10 pages.
##Repeat two more times.  
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##On one graph, plot your three melting curves.
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==Part 1 report outline==
#Pick your favorite of the three melting curves and use your code from the simulation to perform a least squares fit and comment on the results.  
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# Document your circuit design, optical design, and any ways that your instrument differs from the system described in the lab manual.
##What values do you obtain for ΔH and ΔS? Do you trust these values?
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#* Include values for all of the resistors, capacitors in your circuit.
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#* If you have not modified the circuits from their form in the report, you do not need to include the schematic in your report.
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#* Draw a block digram of your optical system, including focal lengths of lenses and key distances.
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#* Include a picture of your instrument.
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# Report your signal to noise measurement.
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# Plot at least one melting curve.  
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#* The plot should have temperature in &deg;C on the horizontal axis and fraction of double stranded DNA on the vertical axis.
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#* On the same set of axes, include a simulated curve generated by DINAMelt, OligoCalc, or another software simulator.
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#* Also on the same set of axes, plot the output of the <tt>DnaFraction</tt> function evaluated with best-fit parameters. You may use nlinfit to choose the best-fit parameters or you may choose them manually. (See: [[DNA Melting: Simulating DNA Melting - Basics]])
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#* Include a legend.
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# Report the estimated melting temperature and the best-fit values of ''&Delta;H&deg;'', ''&Delta;S&deg;''.
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# Explain the statistical method you will use to identify your group's unknown sample in part 2 of this lab.
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#* State the acceptance/rejection criteria for any hypotheses tests you will use.
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#* This page may be a helpful reference: [[Identifying the unknown DNA sample]].
  
 
==Lab manual sections==
 
==Lab manual sections==
  
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*[[Lab Manual:Measuring DNA Melting Curves]]
 
*[[DNA Melting: Simulating DNA Melting - Basics]]
 
*[[DNA Melting: Simulating DNA Melting - Basics]]
 
*[[DNA Melting Part 1: Measuring Temperature and Fluorescence]]
 
*[[DNA Melting Part 1: Measuring Temperature and Fluorescence]]
 
*[[DNA Melting Report Requirements for Part 1]]
 
*[[DNA Melting Report Requirements for Part 1]]
*[[DNA Melting: Simulating DNA Melting - Intermediate Topics]]
 
 
*[[DNA Melting Part 2: Lock-in Amplifier and Temperature Control]]
 
*[[DNA Melting Part 2: Lock-in Amplifier and Temperature Control]]
 
*[[DNA Melting Report Requirements for Part 2]]
 
*[[DNA Melting Report Requirements for Part 2]]
  
 
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Latest revision as of 21:34, 23 March 2017


Report requirements

  • One member of your group should submit a single PDF file to Stellar in advance of the deadline. The filename should consist of the last names of all group members, CamelCased, in alphabetical order, with a .pdf extension. Example: CrickFranklinWatson.pdf.
  • Include answers to questions embedded in the lab manual (e.g. the questions in the RTD section)
  • The file must be less than 20 MB.
  • Include code at the end of the document in an appendix, in the same pdf file, not as as separate upload.
  • Not counting the appendix, your report should be no longer than 10 pages.

Part 1 report outline

  1. Document your circuit design, optical design, and any ways that your instrument differs from the system described in the lab manual.
    • Include values for all of the resistors, capacitors in your circuit.
    • If you have not modified the circuits from their form in the report, you do not need to include the schematic in your report.
    • Draw a block digram of your optical system, including focal lengths of lenses and key distances.
    • Include a picture of your instrument.
  2. Report your signal to noise measurement.
  3. Plot at least one melting curve.
    • The plot should have temperature in °C on the horizontal axis and fraction of double stranded DNA on the vertical axis.
    • On the same set of axes, include a simulated curve generated by DINAMelt, OligoCalc, or another software simulator.
    • Also on the same set of axes, plot the output of the DnaFraction function evaluated with best-fit parameters. You may use nlinfit to choose the best-fit parameters or you may choose them manually. (See: DNA Melting: Simulating DNA Melting - Basics)
    • Include a legend.
  4. Report the estimated melting temperature and the best-fit values of ΔH°, ΔS°.
  5. Explain the statistical method you will use to identify your group's unknown sample in part 2 of this lab.

Lab manual sections

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